CIMseqSinglets: CIMseqSinglets

In jasonserviss/CIMseq: CIMseq is a software suite for analysis of scRNAseq data that has been produced using the cellular interactions by multiplet sequencing method

Description

Subtitle

Usage

getData(x, ...)

## S4 method for signature 'CIMseqSinglets'
getData(x, n = NULL)

getData(x, n) <- value

## S4 replacement method for signature 'CIMseqSinglets'
getData(x, n = NULL) <- value

## S4 method for signature 'CIMseqSinglets'
c(x, ...)

filterSwarm(x, ...)

CIMseqSinglets(counts, ...)

## S4 method for signature 'missing'
CIMseqSinglets(counts, ...)

## S4 method for signature 'matrix'
CIMseqSinglets(counts, counts.ercc, dim.red,
  classification, ...)

## S4 method for signature 'CIMseqSinglets'
initialize(.Object, ..., counts, counts.log,
  counts.cpm, counts.ercc, dim.red, classification)

## S4 method for signature 'CIMseqSinglets'
show(object)

Arguments

x	CIMseqSinglets; CIMseqSinglets object.
...	additional arguments to pass on
n	Data to extract from CIMseqSinglets object.
value	Replacment value.
counts	matrix; Counts matrix with samples as columns and genes as rows.
counts.ercc	matrix; A matrix containing ercc spike-in reads.
dim.red	matrix; Dimensionality reduced representation of the data.
classification	character; Sample classes.
.Object	Internal object.
counts.log	matrix; Log2 normalized counts per million.
counts.cpm	matrix; Normalized counts per million.
object	CIMseqSinglets; A CIMseqSinglets to show.

Details

Imports count, count.ercc, dimensionality reduction, and classification data to a CIMseqSinglets object for sequenced singlets.

Value

CIMseqSinglets object.

Author(s)

Jason T. Serviss

Examples

#setup test data
s <- grepl("^s", colnames(testCounts))
ercc <- grepl("^ERCC\\-[0-9]*$", rownames(testCounts))
singlets <- testCounts[!ercc, s]
singletsERCC <- testCounts[ercc, s]

#dimensionality reduction
select <- selectTopMax(singlets, 100)
pdist <- pearsonsDist(singlets, select)
dim.red <- runTsne(pdist)

#classes
classes <- testMeta$cellTypes[match(colnames(singlets), testMeta$sample)]
#setup CIMseqSinglets object
cObj <- CIMseqSinglets(singlets, singletsERCC, dim.red, classes)

jasonserviss/CIMseq documentation built on Jan. 11, 2020, 4:42 a.m.